Genetics and Genomics of Solanaceae

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (28 February 2021) | Viewed by 21505

Special Issue Editor


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Guest Editor
1. Department of Biotechnology, Institute for Conservation and Improvement of Valencian Agrodiversity (COMAV), School of Agricultural Engineering and Environment (ETSIAMN), Vera Campus, Polytechnic University of Valencia (UPV), Camino de Vera s/n, Building 8E, 4602 Valencia, Spain
2. Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
Interests: plant breeding; Introgression breeding; Crop wild relatives (CWRs); Solanaceae vegetable crops; Genomics; Genetics; Molecular markers; genetic mapping
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Special Issue Information

Dear Colleagues,

The Solanaceae family comprises around 90 genera and 3000–4000 species, and it is considered one of the most important family to humans, as its species are being used as a food source (tomato, potato, pepper, eggplant, pepino dulce, naranjilla, or tamarillo), drugs (tobacco, deadly nightshade, or mandrake), and ornamentals (petunia, velvet tongue, or butterfly flower), among others.
Even though some of these species have received much attention for being widely cultivated and have served as a model crop, the rest have barely been studied and improved, limiting their utilization and conservation.

However, new threats and challenges like climate change, the intensification of abiotic and biotic stresses, and the onset of new pests and diseases are causing yield losses and the deterioration and aridification of cultivation environments, and are jeopardizing the genetic diversity and conservation of many Solanaceous taxa.

At the same time, the urgent need to increase crop yields for the burgeoning world population, the imperative shift towards a climate-smart agriculture to mitigate climate change effects, and the discovery of new drugs and plant products to meet societal demand are only a few of the challenges that need to be addressed by plant scientists.

The aim of this Special Issue is to cover the current genetic and genomic knowledge, from breeding to physiology, from stress screening to conservation, and from drug discovery to in vitro regeneration, which will help gain significant and novel insights into the Solanaceae family.

Dr. Pietro Gramazio
Guest Editor

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Keywords

  • Solanaceae
  • Genomics
  • Genetics
  • Breeding
  • Domestication
  • Conservation
  • Stress response
  • Genome editing

Published Papers (6 papers)

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Research

11 pages, 35971 KiB  
Article
Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport
by Fabien Lombardo, Pietro Gramazio and Hiroshi Ezura
Genes 2021, 12(6), 932; https://doi.org/10.3390/genes12060932 - 18 Jun 2021
Cited by 6 | Viewed by 2395
Abstract
The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of [...] Read more.
The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species. Full article
(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)
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18 pages, 3302 KiB  
Article
Genomic and Phenotypic Diversity of Cultivated and Wild Tomatoes with Varying Levels of Heat Tolerance
by Mathieu Anatole Tele Ayenan, Agyemang Danquah, Paterne A. Agre, Peter Hanson, Isaac Kwadwo Asante and Eric Yirenkyi Danquah
Genes 2021, 12(4), 503; https://doi.org/10.3390/genes12040503 - 29 Mar 2021
Cited by 8 | Viewed by 3141
Abstract
Assessment of genetic variability in heat-tolerant tomato germplasm is a pre-requisite to improve yield and fruit quality under heat stress. We assessed the population structure and diversity in a panel of three Solanum pimpinellifolium (wild tomatoes) and 42 S. lycopersicum (cultivated tomatoes) lines [...] Read more.
Assessment of genetic variability in heat-tolerant tomato germplasm is a pre-requisite to improve yield and fruit quality under heat stress. We assessed the population structure and diversity in a panel of three Solanum pimpinellifolium (wild tomatoes) and 42 S. lycopersicum (cultivated tomatoes) lines and accessions with varying heat tolerance levels. The DArTseq marker was used for the sequencing and 5270 informative single nucleotide polymorphism (SNP) markers were retained for the genomic analysis. The germplasm was evaluated under two heat stress environments for five yield and flower related traits. The phenotypic evaluation revealed moderate broad-sense heritabilities for fruit weight per plant and high broad-sense heritabilities for fruit weight, number of inflorescences per plant, and number of flowers per inflorescence. The hierarchical clustering based on identity by state dissimilarity matrix and UPGMA grouped the germplasm into three clusters. The cluster analysis based on heat-tolerance traits separated the germplasm collection into five clusters. The correlation between the phenotypic and genomic-based distance matrices was low (r = 0.2, p < 0.05). The joint phenotypic and genomic-based clustering grouped the germplasm collection into five clusters well defined for their response to heat stress ranging from highly sensitive to highly tolerant groups. The heat-sensitive and heat-tolerant clusters of S. lycopersicum lines were differentiated by a specific pattern of minor allele frequency distribution on chromosome 11. The joint phenotypic and genomic analysis revealed important diversity within the germplasm collection. This study provides the basis for efficient selection of parental lines to breed heat-tolerant varieties. Full article
(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)
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21 pages, 3177 KiB  
Article
Unravelling Differences in Candidate Genes for Drought Tolerance in Potato (Solanum tuberosum L.) by Use of New Functional Microsatellite Markers
by Christina Schumacher, Christoph Tim Krannich, Lisa Maletzki, Karin Köhl, Joachim Kopka, Heike Sprenger, Dirk Karl Hincha, Sylvia Seddig, Rolf Peters, Sadia Hamera, Ellen Zuther, Manuela Haas and Renate Horn
Genes 2021, 12(4), 494; https://doi.org/10.3390/genes12040494 - 28 Mar 2021
Cited by 9 | Viewed by 3634
Abstract
Potato is regarded as drought sensitive and most vulnerable to climate changes. Its cultivation in drought prone regions or under conditions of more frequent drought periods, especially in subtropical areas, requires intensive research to improve drought tolerance in order to guarantee high yields [...] Read more.
Potato is regarded as drought sensitive and most vulnerable to climate changes. Its cultivation in drought prone regions or under conditions of more frequent drought periods, especially in subtropical areas, requires intensive research to improve drought tolerance in order to guarantee high yields under limited water supplies. A candidate gene approach was used to develop functional simple sequence repeat (SSR) markers for association studies in potato with the aim to enhance breeding for drought tolerance. SSR primer combinations, mostly surrounding interrupted complex and compound repeats, were derived from 103 candidate genes for drought tolerance. Validation of the SSRs was performed in an association panel representing 34 mainly starch potato cultivars. Seventy-five out of 154 SSR primer combinations (49%) resulted in polymorphic, highly reproducible banding patterns with polymorphic information content (PIC) values between 0.11 and 0.90. Five SSR markers identified allelic differences between the potato cultivars that showed significant associations with drought sensitivity. In all cases, the group of drought-sensitive cultivars showed predominantly an additional allele, indicating that selection against these alleles by marker-assisted breeding might confer drought tolerance. Further studies of these differences in the candidate genes will elucidate their role for an improved performance of potatoes under water-limited conditions. Full article
(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)
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15 pages, 3565 KiB  
Article
Comparative Transcriptome Analysis Reveals Key Genes and Pathways Involved in Prickle Development in Eggplant
by Lei Zhang, Haoyun Sun, Tao Xu, Tianye Shi, Zongyun Li and Wenqian Hou
Genes 2021, 12(3), 341; https://doi.org/10.3390/genes12030341 - 25 Feb 2021
Cited by 17 | Viewed by 3611
Abstract
Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis [...] Read more.
Eggplant is one of the most important vegetables worldwide. Prickles on the leaves, stems and fruit calyxes of eggplant may cause difficulties during cultivation, harvesting and transportation, and therefore is an undesirable agronomic trait. However, limited knowledge about molecular mechanisms of prickle morphogenesis has hindered the genetic improvement of eggplant. In this study, we performed the phenotypic characterization and transcriptome analysis on prickly and prickleless eggplant genotypes to understand prickle development at the morphological and molecular levels. Morphological analysis revealed that eggplant prickles were multicellular, lignified and layered organs. Comparative transcriptome analysis identified key pathways and hub genes involved in the cell cycle as well as flavonoid biosynthetic, photosynthetic, and hormone metabolic processes during prickle development. Interestingly, genes associated with flavonoid biosynthesis were up-regulated in developing prickles, and genes associated with photosynthesis were down-regulated in developing and matured prickles. It was also noteworthy that several development-related transcription factors such as bHLH, C2H2, MYB, TCP and WRKY were specifically down- or up-regulated in developing prickles. Furthermore, four genes were found to be differentially expressed within the Pl locus interval. This study provides new insights into the regulatory molecular mechanisms underlying prickle morphogenesis in eggplant, and the genes identified might be exploited in breeding programs to develop prickleless eggplant cultivars. Full article
(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)
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23 pages, 4370 KiB  
Article
Genome-Wide Identification and Expression Profiling of the PDI Gene Family Reveals Their Probable Involvement in Abiotic Stress Tolerance in Tomato (Solanum lycopersicum L.)
by Antt Htet Wai, Muhammad Waseem, A B M Mahbub Morshed Khan, Ujjal Kumar Nath, Do Jin Lee, Sang Tae Kim, Chang Kil Kim and Mi Young Chung
Genes 2021, 12(1), 23; https://doi.org/10.3390/genes12010023 - 25 Dec 2020
Cited by 15 | Viewed by 3624
Abstract
Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of [...] Read more.
Protein disulfide isomerases (PDI) and PDI-like proteins catalyze the formation and isomerization of protein disulfide bonds in the endoplasmic reticulum and prevent the buildup of misfolded proteins under abiotic stress conditions. In the present study, we conducted the first comprehensive genome-wide exploration of the PDI gene family in tomato (Solanum lycopersicum L.). We identified 19 tomato PDI genes that were unevenly distributed on 8 of the 12 tomato chromosomes, with segmental duplications detected for 3 paralogous gene pairs. Expression profiling of the PDI genes revealed that most of them were differentially expressed across different organs and developmental stages of the fruit. Furthermore, most of the PDI genes were highly induced by heat, salt, and abscisic acid (ABA) treatments, while relatively few of the genes were induced by cold and nutrient and water deficit (NWD) stresses. The predominant expression of SlPDI1-1, SlPDI1-3, SlPDI1-4, SlPDI2-1, SlPDI4-1, and SlPDI5-1 in response to abiotic stress and ABA treatment suggested they play regulatory roles in abiotic stress tolerance in tomato in an ABA-dependent manner. Our results provide new insight into the structure and function of PDI genes and will be helpful for the selection of candidate genes involved in fruit development and abiotic stress tolerance in tomato. Full article
(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)
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20 pages, 4914 KiB  
Article
Genome-Wide Identification, Classification, Characterization, and Expression Analysis of the Wall-Associated Kinase Family during Fruit Development and under Wound Stress in Tomato (Solanum lycopersicum L.)
by Zongyan Sun, Yanping Song, Di Chen, Yudi Zang, Qiaoli Zhang, Yuetong Yi and Guiqin Qu
Genes 2020, 11(10), 1186; https://doi.org/10.3390/genes11101186 - 12 Oct 2020
Cited by 26 | Viewed by 4100
Abstract
The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively [...] Read more.
The wall-associated kinase (WAK) and wall-associated kinase like (WAKL) is a subfamily of receptor-like kinases associated with the cell wall, which have been suggested as sensors of the extracellular environment and triggers of intracellular signals. However, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum L.). In this study, 11 SlWAK and 18 SlWAKL genes were identified in an uneven distribution in 9 of 12 chromosomes. GUB-WAK-bind (wall-associated receptor kinase galacturonan-binding) and epidermal growth factor (EGF) domains appear more often in SlWAK proteins. However, more SlWAKLs (wall-associated kinase like) have a WAK-assoc (wall-associated receptor kinase C-terminal) domain. Based on their phylogenetic relationships, 29 SlWAK-RLKs (wall associated kinase-receptor like kinases) were clustered into three distinct categories analogous to those in Arabidopsis thaliana. High similarities were found in conserved motifs of the genes within each group. Cis-elements in the promoter region of these 29 genes were found mainly in response to methyl jasmonate (MeJA), abscisic acid (ABA), salicylic acid (SA), anaerobic, light, wound, and MYB transcription factors. Public tomato genome RNA-seq data indicates that multiple SlWAK-RLKs showed different expression patterns under developmental and ripening stages of fruits, such as SlWAK4, SlWAKL11, SlWAKL9, SlWAKL15, SlWAKL14, and SlWAKL1, their RPKM (Reads Per Kilo bases per Million reads) value constantly increases during the fruit expansion period, and decreases as the fruit matures. In tomato leaves, our RNA-seq data showed that nine SlWAK-RLKs transcripts (SlWAK3, SlWAK4, SlWAK10,SlWAKL1, SlWAKL2, SlWAKL3, SlWAKL5, SlWAKL14, and SlWAKL18) were significantly induced (p < 0.001), and three transcripts (SlWAK2, SlWAK5, and SlWAKL15) were significantly inhibited (p < 0.001) under mechanical wounding. The qRT-PCR (Quantitative reverse transcription polymerase chain reaction) of SlWAKL1 and SlWAKL6 verify these results. Full article
(This article belongs to the Special Issue Genetics and Genomics of Solanaceae)
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